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Fwd: [nanoporetech/dorado] Release v0.9.1 - v0.9.1
by Marco van Zwetselaar 21 Jan '25

21 Jan '25

FYI, a new Dorado basecaller is out, supposedly much faster on newer GPUs, and now with flag --bacteria that uses models optimised for bacterial DNA. ONT are also working toward integrating Medaka in Dorado, as discussed here[1], but this is currently still beta-level. Best wishes, Marco [1] https://github.com/nanoporetech/medaka/issues/546 -------- Forwarded Message -------- Subject: [nanoporetech/dorado] Release v0.9.1 - v0.9.1 Date: Tue, 21 Jan 2025 06:55:17 -0800 From: Chris Seymour [<notifications(a)github.com>](mailto:notifications@github.com) Reply-To: nanoporetech/dorado [<noreply(a)github.com>](mailto:noreply@github.com) To: nanoporetech/dorado [<dorado(a)noreply.github.com>](mailto:dorado@noreply.github.com) CC: Subscribed [<subscribed(a)noreply.github.com>](mailto:subscribed@noreply.github.com) [v0.9.1](https://github.com/nanoporetech/dorado/releases/tag/v0.9.1) Repository: [nanoporetech/dorado](https://github.com/nanoporetech/dorado) · Tag: [v0.9.1](https://github.com/nanoporetech/dorado/tree/v0.9.1) · Commit: [77b58fe](https://github.com/nanoporetech/dorado/commit/77b58fead2827517ac4b… · Released by: [iiSeymour](https://github.com/iiSeymour) [0.9.1] (21 Jan 2025) This release of Dorado brings significant basecalling speed improvements for Nvidia GPUs with compute capabilities 8.6 (Ampere – e.g., RTX A6000), 8.7 (Ampere – e.g., Orin family), and 8.9 (Ada Lovelace). Additionally, dorado polish receives major enhancements, including the introduction of the --bacteria flag, which optimizes basecalling for native bacterial and methylated DNA. The updated dorado polish is now compatible with data basecalled using v4.3 and v4.2 models and serves as a beta-stage replacement for Medaka. - [d46286e](https://github.com/nanoporetech/dorado/commit/d46286e9e9f549b2f776… - Upgraded to Koi v0.5.3 for optimised basecalling on CC 8.6, 8.7 & 8.9 - 6de083d977a0f33398fb1f82e9e0df621ea5360b - Added VCF output to the Dorado polish - [d859977](https://github.com/nanoporetech/dorado/commit/d8599772fdc2e7c3374c… - Improve messaging when an unrecognised model complex is specified - [06f6239](https://github.com/nanoporetech/dorado/commit/06f62390bdd5cbbf024b… - Support for legacy count models in Dorado polish - [e51d64f](https://github.com/nanoporetech/dorado/commit/e51d64fe88aa9dee9982… - Fixed precision issue with Dorado polish qscore normalisation - [d50494d](https://github.com/nanoporetech/dorado/commit/d50494d16c27d3e40228… - Added --bacteria support for Dorado polish - [f3fa447](https://github.com/nanoporetech/dorado/commit/f3fa4473a6eec4224be6… - Added ULK114 kits to adapter/primer trimming LUT - [1a4316e](https://github.com/nanoporetech/dorado/commit/1a4316efc3d589ebfa5e… - Dorado polish algorithm improvements and refactoring - [a0fc960](https://github.com/nanoporetech/dorado/commit/a0fc96001862ac751b23… - Dorado polish option -o now writes to a directory - [7ae31a8](https://github.com/nanoporetech/dorado/commit/7ae31a85018287fdf407… - Dorado polish fix for parsing FASTA file inputs - [b382344](https://github.com/nanoporetech/dorado/commit/b382344de58bf10ed07e… - Dorado polish models are now included in Dorado download --list, --list-yaml, and --list-structured - [adebcc5](https://github.com/nanoporetech/dorado/commit/adebcc5346c209888d32… - Ensure Q-score and read length filters are applied to reads after trimming - [96d574d](https://github.com/nanoporetech/dorado/commit/96d574d9658c00968113… - Enforce use of --kit-name for Dorado demux custom barcodes to prevent unclassified reads - [62c86d0](https://github.com/nanoporetech/dorado/commit/62c86d08a4cceee470f2… - Support CUDA_VISIBLE_DEVICES for UUIDs or integers - [c39f906](https://github.com/nanoporetech/dorado/commit/c39f9064f200ca4cc9f2… - Prevent crashing in auto batchsize due to short chunksizes — This release has 2 assets: - Source code (zip) - Source code (tar.gz) Visit the [release page](https://github.com/nanoporetech/dorado/releases/tag/v0.9.1) to download them. — You are receiving this because you are watching this repository. [View it on GitHub](https://github.com/nanoporetech/dorado/releases/tag/v0.9.1) or [unsubscribe](https://github.com/nanoporetech/dorado/unsubscribe_via_email/A… from all notifications for this repository.

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BenchAMRking: [...] illustrating the major issues associated with current antimicrobial resistance (AMR) gene prediction workflows
by Marco van Zwetselaar 16 Jan '25

16 Jan '25

Dear all, Oh no, not another tool with an AMRwkward name! Wasn't hAMRonization enough already? (Try typing it if you disagree.) But anyway, this looks like a valuable initiative: Strepis N, Dollee D, Vrins D, Vanneste K, Bogaerts B, Carrillo C, et al. BenchAMRking: a Galaxy-based platform for illustrating the major issues associated with current antimicrobial resistance (AMR) gene prediction workflows. BMC Genomics. 2025;26: 27. doi:10.1186/s12864-024-11158-5. https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-024-11158-5 I was a bit underwhelmed by the four currently included workflows (see: https://erasmusmc-bioinformatics.github.io/benchAMRking/) of which two are Salmonella-only, one Ecoli-only, and one multi-species (abritAMR), but things can grow from here. How does it relate to hARMonization_workflow, which incorporates 18 AMR tools? BenchAMRking aims at validating AMR workflows for clinical and public health use, against a "gold standard" reference. hAMRonization_workflow was set up primarily to have a testing ground for hAMRonization, the tool to convert output from any AMR tool into a common format. As its maintainer (Finlay Maguire) said, the workflow is almost too brittle to maintain. But how else will you test hAMRonization, manually run 18 tools over a dozen inputs?! I recently submitted a bunch of patches to bring hAMRonization up to date with the latest tool versions. I also managed to upgrade hAMRonization_workflow to use all the latest tool versions. Give it a try if you're up for it: https://github.com/pha4ge/hAMRonization_workflow. It installs with a simple "conda env create". Prepare for a long wait on the first run, while it installs all tools and databases. Subsequent runs are quick: it takes ~10mn on my laptop to run all 18 tools on an isolate. Best wishes, AMRco ;-)

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Reminder: SeqAfrica January Bioinformatics CoP – Results from the genomic proficiency tests 2020-2022
by Pernille Nilsson 08 Jan '25

08 Jan '25

Dear Bioinformatics Community of Practice Members, Happy New Year and wishes for a fantastic 2025! We are excited to inform you of this year’s first Bioinformatics Community of Practice session tomorrow, where Niamh Lacy-Roberts will present the results from her draft paper titled “Whole Genome Sequencing Proficiency in African Laboratories for Antimicrobial Resistance Surveillance: Results of the SeqAfrica 2020-2022 Genomic Proficiency Tests”. Niamh would also welcome your feedback on the plots, results, and conclusions. This is a great opportunity to learn more about the progress of the genomic proficiency testing conducted in SeqAfrica and we are excited for your input! Best wishes, Pernille [signature_693501174] Dr Pernille Nilsson Pronouns: she, her Project Manager SeqAfrica National Food Institute Research Group for Global Capacity Building Mob. +45 93 51 16 54 pnil(a)food.dtu.dk<mailto:pnil@food.dtu.dk> Henrik Dams Allé Building 204 2800 Kgs. Lyngby www.food.dtu.dk<http://www.food.dtu.dk>

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Reminder: Bioinformatics COP tomorrow!
by Christa Twyford Gibson 04 Dec '24

04 Dec '24

Hello all, Just a gentle reminder that our bioinformatics community of practice meets tomorrow at 12:30 CET. We look forward to seeing you all there! Please see the zoom info below! Warm Regards, Christa [cid:image001.png@01DB4675.B26FA220] Christa Twyford Gibson Project Manager for SeqAfrica Project Fleming Fund Regional Grant SeqAfrica (dtu.dk)<https://www.food.dtu.dk/english/topics/antimicrobial-resistance/seqafrica> chrgi(a)dtu.dk<mailto:chrgi@dtu.dk> +45 53 81 91 15 National Food Institute Research Group for Global Capacity Building Building 204 Henrik Dams Allé 2800 Kgs. Lyngby www.food.dtu.dk<http://www.food.dtu.dk/> Monthly: https://dtudk.zoom.us/meeting/u5wuceygpjwiGdEbcHdEjNfGTVqdz4TigrBi/ics?icsT… Join Zoom Meeting https://dtudk.zoom.us/j/68365887835 Meeting ID: 683 6588 7835 --- One tap mobile +4589883788,,68365887835# Denmark +4532701206,,68365887835# Denmark --- Dial by your location • +45 89 88 37 88 Denmark • +45 32 70 12 06 Denmark • +45 32 71 31 57 Denmark • +45 32 72 80 10 Denmark • +45 32 72 80 11 Denmark • +45 47 37 25 75 Denmark Meeting ID: 683 6588 7835 Find your local number: https://dtudk.zoom.us/u/ccDieRpbcq --- Join by SIP 68365887835(a)109.105.112.236<mailto:68365887835@109.105.112.236> • 68365887835(a)109.105.112.235<mailto:68365887835@109.105.112.235> --- Join by H.323 • 109.105.112.236 • 109.105.112.235 Meeting ID: 683 6588 7835

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African Bioinformatics Institute
by Marco van Zwetselaar 07 Nov '24

07 Nov '24

Dear all, Thank you all for joining today's CoP meeting, and in particular Adja for presenting the bacterial analysis pipeline developed at Institut Pasteur de Dakar! As mentioned in today's meeting, here is a link to the "African Bioinformatics Insititute" initiative: https://wellcome.org/news/were-establishing-new-institute-advance-genomics-… An in-person and virtual stakeholder meeting will take place in Cape Town on 29-30 January: https://redcap.h3abionet.org/redcap/surveys/?s=M8CWTNPP9DLC37Y9 You can express your interesting in hosting an ABI Node here: https://redcap.h3abionet.org/redcap/surveys/?s=RAA4ERLP3KNTEMKE And finally, there is an open call for the position of director here: https://tinyurl.com/yn663vm2 With thanks to @Niamh Lacy-Roberts for passing on this information Kind regards, Marco

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Join the Bioinformatics COP now!
by Christa Twyford Gibson 07 Nov '24

07 Nov '24

Hi all, We are kicking off our November Bioinformatics COP now! Please join us online here: Join Zoom Meeting https://dtudk.zoom.us/j/68365887835 Cheers, christa [cid:image001.png@01DB3111.5D825830] Christa Twyford Gibson Project Manager for SeqAfrica Project Fleming Fund Regional Grant SeqAfrica (dtu.dk)<https://www.food.dtu.dk/english/topics/antimicrobial-resistance/seqafrica> chrgi(a)dtu.dk<mailto:chrgi@dtu.dk> +45 53 81 91 15 National Food Institute Research Group for Global Capacity Building Building 204 Henrik Dams Allé 2800 Kgs. Lyngby www.food.dtu.dk<http://www.food.dtu.dk/>

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ONT beats Illumina at variant calling ...
by Marco van Zwetselaar 07 Nov '24

07 Nov '24

... or so the authors* claim in this paper: Hall MB, Wick RR, Judd LM, Nguyen AN, Steinig EJ, Xie O, et al. Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data. Weigel D, editor. eLife. 2024;13: RP98300. doi:[10.7554/eLife.98300](https://doi.org/10.7554/eLife.98300) > This important study shows how a combination of the latest generation of Oxford Nanopore Technology long reads with state-of-the art variant callers enables bacterial variant discovery at an accuracy that matches or exceeds the current "gold standard" with short reads. The work thus heralds a new era, in which Illumina short-read sequencing no longer rules supreme. [Source: publisher's assessment, my emphasis.] *) Including bioinformatics superheroes Ryan Wick and Torsten Seemann :) Cheers Marco PS: hope to see you all at the CoP meeting in 2 hours: https://dtudk.zoom.us/j/68365887835

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Metagenomic assemblies tend to break around antibiotic resistance genes
by Marco van Zwetselaar 28 Oct '24

28 Oct '24

Abramova A, Karkman A, Bengtsson-Palme J. Metagenomic assemblies tend to break around antibiotic resistance genes. BMC Genomics. 2024;25: 959. doi:[10.1186/s12864-024-10876-0](https://doi.org/10.1186/s12864-024-10876-0) @Philip I seem to recall a paper from DTU on a tool that tried to solve precisely the issue your eastern neighbours stumble over in this paper? Cheers Marco

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When less is more: sketching with minimizers in genomics
by Marco van Zwetselaar 26 Oct '24

26 Oct '24

Comprehensive overview article on minimizers and how they are used in current tools for alignment, assembly, etc. Great for catching up on some foundational bioinformatics. ;-) Ndiaye M, Prieto-Baños S, Fitzgerald LM, Yazdizadeh Kharrazi A, Oreshkov S, Dessimoz C, et al. When less is more: sketching with minimizers in genomics. Genome Biology. 2024;25:270. https://doi.org/10.1186/s13059-024-03414-4 Cheers Marco

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Updated time for SeqAfrica Bioinformatics Community of Practice: 11:30 UTC/12:30 CET
by Christa Twyford Gibson 23 Oct '24

23 Oct '24

Hi all, Please note the change in time to our monthly SeqAfrica Bioinformatics Community of Practice. We will now be meeting at 11:30 UTC/12:30 CET. We look forward to seeing you at our next meeting on November 7! As always you can find us on Zoom at the link below. Cheers, Christa Christa Gibson is inviting you to a scheduled Zoom meeting. Join Zoom Meeting https://dtudk.zoom.us/j/68365887835 Meeting ID: 683 6588 7835 [cid:image001.png@01DB2527.3AA13FC0] Christa Twyford Gibson Project Manager for SeqAfrica Project Fleming Fund Regional Grant SeqAfrica (dtu.dk)<https://www.food.dtu.dk/english/topics/antimicrobial-resistance/seqafrica> chrgi(a)dtu.dk<mailto:chrgi@dtu.dk> +45 53 81 91 15 National Food Institute Research Group for Global Capacity Building Building 204 Henrik Dams Allé 2800 Kgs. Lyngby www.food.dtu.dk<http://www.food.dtu.dk/>

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2026

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2024